FMO DATABASE

FMODB ID: 82GMY

Calculation Name: 1EM8-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1EM8

Chain ID: B

ChEMBL ID:

UniProt ID: P28905

Base Structure: X-ray

Registration Date: 2023-03-13

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	110
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-816517.254035
FMO2-HF: Nuclear repulsion	774457.175615
FMO2-HF: Total energy	-42060.078419
FMO2-MP2: Total energy	-42182.210301

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(B:27:GLY)

Summations of interaction energy for fragment #1(B:27:GLY)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
2.074	3.742	-0.009	-0.882	-0.777	0.001

Interaction energy analysis for fragmet #1(B:27:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : 0.006

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	B	29	ILE	0	-0.050	-0.019	3.749	0.975	2.643	-0.009	-0.882	-0.777	0.001
4	B	30	ALA	0	0.016	0.012	5.214	0.308	0.308	0.000	0.000	0.000	0.000
5	B	31	ILE	0	-0.048	-0.031	6.948	0.142	0.142	0.000	0.000	0.000	0.000
6	B	32	ALA	0	0.019	0.003	10.591	0.077	0.077	0.000	0.000	0.000	0.000
7	B	33	ILE	0	0.032	0.013	12.140	0.086	0.086	0.000	0.000	0.000	0.000
8	B	34	PRO	0	-0.008	-0.004	15.290	-0.021	-0.021	0.000	0.000	0.000	0.000
9	B	35	ALA	0	0.053	0.021	18.446	0.033	0.033	0.000	0.000	0.000	0.000
10	B	36	HIS	0	-0.028	-0.010	20.459	0.007	0.007	0.000	0.000	0.000	0.000
11	B	37	VAL	0	-0.030	-0.004	19.424	0.026	0.026	0.000	0.000	0.000	0.000
12	B	38	ARG	1	0.804	0.882	21.531	0.194	0.194	0.000	0.000	0.000	0.000
13	B	39	LEU	0	0.004	0.015	22.709	0.018	0.018	0.000	0.000	0.000	0.000
14	B	40	VAL	0	0.019	0.014	16.913	-0.018	-0.018	0.000	0.000	0.000	0.000
15	B	41	MET	0	-0.027	-0.001	20.077	0.024	0.024	0.000	0.000	0.000	0.000
16	B	42	VAL	0	0.009	0.005	18.372	-0.009	-0.009	0.000	0.000	0.000	0.000
17	B	43	ALA	0	0.033	0.010	21.127	0.012	0.012	0.000	0.000	0.000	0.000
18	B	44	ASN	0	0.011	-0.003	22.035	0.005	0.005	0.000	0.000	0.000	0.000
19	B	45	ASP	-1	-0.910	-0.953	23.388	0.027	0.027	0.000	0.000	0.000	0.000
20	B	46	LEU	0	-0.050	-0.021	20.585	-0.005	-0.005	0.000	0.000	0.000	0.000
21	B	47	PRO	0	0.008	0.017	25.123	-0.004	-0.004	0.000	0.000	0.000	0.000
22	B	48	ALA	0	0.028	0.011	27.866	-0.011	-0.011	0.000	0.000	0.000	0.000
23	B	49	LEU	0	0.033	0.004	26.012	0.008	0.008	0.000	0.000	0.000	0.000
24	B	50	THR	0	-0.008	-0.004	30.034	-0.001	-0.001	0.000	0.000	0.000	0.000
25	B	51	ASP	-1	-0.798	-0.883	33.036	-0.014	-0.014	0.000	0.000	0.000	0.000
26	B	52	PRO	0	-0.004	-0.011	34.833	-0.002	-0.002	0.000	0.000	0.000	0.000
27	B	53	LEU	0	0.016	0.022	34.417	-0.001	-0.001	0.000	0.000	0.000	0.000
28	B	54	VAL	0	0.004	0.002	29.571	0.001	0.001	0.000	0.000	0.000	0.000
29	B	55	SER	0	0.004	0.006	32.055	-0.004	-0.004	0.000	0.000	0.000	0.000
30	B	56	ASP	-1	-0.844	-0.923	34.151	-0.032	-0.032	0.000	0.000	0.000	0.000
31	B	57	VAL	0	-0.046	-0.016	30.551	0.001	0.001	0.000	0.000	0.000	0.000
32	B	58	LEU	0	-0.002	0.001	27.583	-0.001	-0.001	0.000	0.000	0.000	0.000
33	B	59	ARG	1	0.862	0.921	31.334	0.041	0.041	0.000	0.000	0.000	0.000
34	B	60	ALA	0	-0.034	-0.013	34.282	-0.001	-0.001	0.000	0.000	0.000	0.000
35	B	61	LEU	0	0.004	-0.008	27.843	0.002	0.002	0.000	0.000	0.000	0.000
36	B	62	THR	0	-0.073	-0.032	30.854	-0.005	-0.005	0.000	0.000	0.000	0.000
37	B	63	VAL	0	-0.026	-0.003	26.691	-0.008	-0.008	0.000	0.000	0.000	0.000
38	B	64	SER	0	0.005	-0.021	29.926	0.010	0.010	0.000	0.000	0.000	0.000
39	B	65	PRO	0	0.007	-0.013	28.476	-0.008	-0.008	0.000	0.000	0.000	0.000
40	B	66	ASP	-1	-0.844	-0.906	26.983	-0.126	-0.126	0.000	0.000	0.000	0.000
41	B	67	GLN	0	-0.046	-0.019	24.842	-0.011	-0.011	0.000	0.000	0.000	0.000
42	B	68	VAL	0	0.023	0.010	23.444	-0.001	-0.001	0.000	0.000	0.000	0.000
43	B	69	LEU	0	-0.005	0.007	15.655	-0.013	-0.013	0.000	0.000	0.000	0.000
44	B	70	GLN	0	-0.045	-0.049	19.865	0.013	0.013	0.000	0.000	0.000	0.000
45	B	71	LEU	0	-0.013	-0.010	14.408	-0.030	-0.030	0.000	0.000	0.000	0.000
46	B	72	THR	0	0.015	-0.018	17.762	0.009	0.009	0.000	0.000	0.000	0.000
47	B	73	PRO	0	0.046	0.008	16.427	-0.006	-0.006	0.000	0.000	0.000	0.000
48	B	74	GLU	-1	-0.824	-0.868	14.358	0.085	0.085	0.000	0.000	0.000	0.000
49	B	75	LYS	1	0.844	0.899	12.109	0.119	0.119	0.000	0.000	0.000	0.000
50	B	76	ILE	0	-0.007	0.003	11.567	-0.084	-0.084	0.000	0.000	0.000	0.000
51	B	77	ALA	0	0.011	0.012	9.689	-0.013	-0.013	0.000	0.000	0.000	0.000
52	B	78	MET	0	-0.045	-0.017	7.219	0.222	0.222	0.000	0.000	0.000	0.000
53	B	79	LEU	0	0.005	0.025	7.820	-0.401	-0.401	0.000	0.000	0.000	0.000
54	B	80	PRO	0	-0.009	0.013	6.319	0.047	0.047	0.000	0.000	0.000	0.000
55	B	81	GLN	0	0.028	0.005	6.392	0.205	0.205	0.000	0.000	0.000	0.000
56	B	82	GLY	0	0.021	0.015	8.230	-0.179	-0.179	0.000	0.000	0.000	0.000
57	B	83	SER	0	-0.067	-0.044	10.514	-0.046	-0.046	0.000	0.000	0.000	0.000
58	B	84	HIS	0	0.010	0.001	12.890	0.083	0.083	0.000	0.000	0.000	0.000
59	B	85	CYS	0	-0.060	-0.034	16.691	-0.041	-0.041	0.000	0.000	0.000	0.000
60	B	86	ASN	0	0.010	0.039	19.143	0.026	0.026	0.000	0.000	0.000	0.000
61	B	87	SER	0	0.007	0.003	19.850	-0.011	-0.011	0.000	0.000	0.000	0.000
62	B	88	TRP	0	0.024	-0.006	22.002	0.006	0.006	0.000	0.000	0.000	0.000
63	B	89	ARG	1	0.864	0.944	21.386	-0.115	-0.115	0.000	0.000	0.000	0.000
64	B	90	LEU	0	-0.021	-0.010	23.635	0.002	0.002	0.000	0.000	0.000	0.000
65	B	91	GLY	0	-0.053	-0.026	25.192	0.004	0.004	0.000	0.000	0.000	0.000
66	B	92	THR	0	-0.036	-0.034	20.505	0.011	0.011	0.000	0.000	0.000	0.000
67	B	93	ASP	-1	-0.914	-0.957	23.432	0.127	0.127	0.000	0.000	0.000	0.000
68	B	94	GLU	-1	-0.903	-0.942	19.449	0.270	0.270	0.000	0.000	0.000	0.000
69	B	95	PRO	0	-0.042	-0.023	19.607	-0.020	-0.020	0.000	0.000	0.000	0.000
70	B	96	LEU	0	0.001	0.005	16.525	0.031	0.031	0.000	0.000	0.000	0.000
71	B	97	SER	0	0.001	0.007	11.789	0.019	0.019	0.000	0.000	0.000	0.000
72	B	98	LEU	0	-0.075	-0.044	12.574	-0.029	-0.029	0.000	0.000	0.000	0.000
73	B	99	GLU	-1	-0.907	-0.939	15.030	0.104	0.104	0.000	0.000	0.000	0.000
74	B	100	GLY	0	0.047	0.010	17.309	-0.039	-0.039	0.000	0.000	0.000	0.000
75	B	101	ALA	0	-0.006	0.010	20.801	0.024	0.024	0.000	0.000	0.000	0.000
76	B	102	GLN	0	-0.018	-0.017	18.338	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	103	VAL	0	0.003	0.008	23.387	0.011	0.011	0.000	0.000	0.000	0.000
78	B	104	ALA	0	0.025	0.007	25.023	0.002	0.002	0.000	0.000	0.000	0.000
79	B	105	SER	0	-0.021	-0.008	26.917	-0.008	-0.008	0.000	0.000	0.000	0.000
80	B	106	PRO	0	0.037	0.010	28.409	0.006	0.006	0.000	0.000	0.000	0.000
81	B	107	ALA	0	0.090	0.055	29.084	-0.005	-0.005	0.000	0.000	0.000	0.000
82	B	108	LEU	0	0.017	0.003	29.964	-0.002	-0.002	0.000	0.000	0.000	0.000
83	B	109	THR	0	-0.023	-0.015	31.785	-0.005	-0.005	0.000	0.000	0.000	0.000
84	B	110	ASP	-1	-0.818	-0.923	32.892	0.043	0.043	0.000	0.000	0.000	0.000
85	B	111	LEU	0	-0.025	-0.002	31.595	-0.002	-0.002	0.000	0.000	0.000	0.000
86	B	112	ARG	1	0.893	0.925	34.406	0.001	0.001	0.000	0.000	0.000	0.000
87	B	113	ALA	0	-0.005	0.006	37.486	-0.002	-0.002	0.000	0.000	0.000	0.000
88	B	114	ASN	0	0.002	0.010	37.628	-0.002	-0.002	0.000	0.000	0.000	0.000
89	B	115	PRO	0	0.023	-0.005	38.616	-0.001	-0.001	0.000	0.000	0.000	0.000
90	B	116	THR	0	0.029	0.016	39.799	-0.003	-0.003	0.000	0.000	0.000	0.000
91	B	117	ALA	0	0.005	0.010	34.865	0.001	0.001	0.000	0.000	0.000	0.000
92	B	118	ARG	1	0.878	0.928	35.206	-0.007	-0.007	0.000	0.000	0.000	0.000
93	B	119	ALA	0	-0.014	0.001	36.420	-0.003	-0.003	0.000	0.000	0.000	0.000
94	B	120	ALA	0	0.032	0.011	35.009	-0.001	-0.001	0.000	0.000	0.000	0.000
95	B	121	LEU	0	-0.003	0.008	30.785	0.002	0.002	0.000	0.000	0.000	0.000
96	B	122	TRP	0	0.022	0.003	32.781	-0.002	-0.002	0.000	0.000	0.000	0.000
97	B	123	GLN	0	0.007	0.006	35.213	0.000	0.000	0.000	0.000	0.000	0.000
98	B	124	GLN	0	0.008	0.001	28.821	0.003	0.003	0.000	0.000	0.000	0.000
99	B	125	ILE	0	0.002	0.000	30.580	-0.002	-0.002	0.000	0.000	0.000	0.000
100	B	126	CYS	0	-0.072	-0.036	32.063	-0.004	-0.004	0.000	0.000	0.000	0.000
101	B	127	THR	0	-0.053	-0.034	31.294	0.000	0.000	0.000	0.000	0.000	0.000
102	B	128	TYR	0	-0.022	-0.005	25.970	0.004	0.004	0.000	0.000	0.000	0.000
103	B	129	GLU	-1	-0.847	-0.914	30.388	-0.021	-0.021	0.000	0.000	0.000	0.000
104	B	130	HIS	0	-0.052	-0.025	30.721	-0.012	-0.012	0.000	0.000	0.000	0.000
105	B	131	ASP	-1	-0.875	-0.933	26.246	-0.024	-0.024	0.000	0.000	0.000	0.000
106	B	132	PHE	0	-0.034	-0.030	25.678	-0.013	-0.013	0.000	0.000	0.000	0.000
107	B	133	PHE	0	-0.022	0.009	29.668	-0.004	-0.004	0.000	0.000	0.000	0.000
108	B	134	PRO	0	-0.002	0.013	29.966	0.004	0.004	0.000	0.000	0.000	0.000
109	B	135	ARG	1	0.802	0.866	32.824	0.026	0.026	0.000	0.000	0.000	0.000
110	B	136	ASN	0	-0.029	-0.004	36.110	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:27:GLY)